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Luesken F.A.,Radboud University Nijmegen | Wu M.L.,Radboud University Nijmegen | Op den Camp H.J.M.,Radboud University Nijmegen | Keltjens J.T.,Radboud University Nijmegen | And 5 more authors.
Environmental Microbiology | Year: 2012

'Candidatus Methylomirabilis oxyfera' is a denitrifying methanotroph that performs nitrite-dependent anaerobic methane oxidation through a newly discovered intra-aerobic pathway. In this study, we investigated the response of a M.oxyfera enrichment culture to oxygen. Addition of either 2% or 8% oxygen resulted in an instant decrease of methane and nitrite conversion rates. Oxygen exposure also led to a deviation in the nitrite to methane oxidation stoichiometry. Oxygen-uptake and inhibition studies with cell-free extracts displayed a change from cytochrome c to quinol as electron donor after exposure to oxygen. The change in global gene expression was monitored by deep sequencing of cDNA using Illumina technology. After 24h of oxygen exposure, transcription levels of 1109 (out of 2303) genes changed significantly when compared with the anoxic period. Most of the genes encoding enzymes of the methane oxidation pathway were constitutively expressed. Genes from the denitrification pathway, with exception of one of the putative nitric oxide reductases, norZ2, were severely downregulated. The majority of known genes involved in the vital cellular functions, such as nucleic acid and protein biosynthesis and cell division processes, were downregulated. The alkyl hydroperoxide reductase, ahpC, and genes involved in the synthesis/repair of the iron-sulfur clusters were among the few upregulated genes. Further, transcription of the pmoCAB genes of aerobic methanotrophs present in the non-M.oxyfera community were triggered by the presence of oxygen. Our results show that oxygen-exposed cells of M.oxyfera were under oxidative stress and that in spite of its oxygenic capacity, exposure to microoxic conditions has an overall detrimental effect. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Monismith S.G.,Stanford University | Herdman L.M.M.,Stanford University | Ahmerkamp S.,MPI for Marine Microbiology | Hench J.L.,Stanford University | Hench J.L.,Duke University
Journal of Physical Oceanography | Year: 2013

Observations of waves, setup, and wave-driven mean flows were made on a steep coral forereef and its associated lagoonal system on the north shore of Moorea, French Polynesia. Despite the steep and complex geometry of the forereef, and wave amplitudes that are nearly equal to the mean water depth, linear wave theory showed very good agreement with data. Measurements across the reef illustrate the importance of including both wave transport (owing to Stokes drift), as well as the Eulerian mean transport when computing the fluxes over the reef. Finally, the observed setup closely follows the theoretical relationship derived from classic radiation stress theory, although the two parameters that appear in the model-one reflecting wave breaking, the other the effective depth over the reef crest-must be chosen to match theory to data. © 2013 American Meteorological Society.

Gilbert J.A.,Argonne National Laboratory | Gilbert J.A.,University of Chicago | Meyer F.,Argonne National Laboratory | Meyer F.,University of Chicago | And 16 more authors.
Standards in Genomic Sciences | Year: 2010

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6 th 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world.

Wu M.L.,Radboud University Nijmegen | van Alen T.A.,Radboud University Nijmegen | van Donselaar E.G.,University Utrecht | Strous M.,MPI for Marine Microbiology | And 3 more authors.
FEMS Microbiology Letters | Year: 2012

'Candidatus Methylomirabilis oxyfera'; is a polygon-shaped bacterium that was shown to have the unique ability to couple anaerobic methane oxidation to denitrification, through a newly discovered intra-aerobic pathway. Recently, the complete genome of Methylomirabilis oxyfera was assembled into a 2.7-Mb circular single chromosome by metagenomic sequencing. The genome of M. oxyfera revealed the full potential to perform both methane oxidation and the conversion of nitrite via nitric oxide into oxygen and dinitrogen gas. In this study, we show by immunogold localization that key enzymes from both methane- and nitrite-converting pathways are indeed present in single M. oxyfera cells. Antisera targeting the particulate methane monooxygenase (pMMO) and the cd1 nitrite reductase (NirS) were raised and used for immunogold localization in both single- and double-labelling experiments. Our previous studies have shown that M. oxyfera does not develop pMMO-containing intracytoplasmic membranes as is observed in classical proteobacterial methanotrophs. Our results suggest that in M. oxyfera, the pMMO and NirS enzymes localized to the cytoplasmic membrane and periplasm, respectively. Further, double-labelling showed co-occurrence of pMMO and NirS in single M. oxyfera cells. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Wu M.L.,Radboud University Nijmegen | Van Teeseling M.C.F.,Radboud University Nijmegen | Willems M.J.R.,Radboud University Nijmegen | Van Donselaar E.G.,University Utrecht | And 8 more authors.
Journal of Bacteriology | Year: 2012

"Candidatus Methylomirabilis oxyfera" is a newly discovered denitrifying methanotroph that is unrelated to previously known methanotrophs. This bacterium is a member of the NC10 phylum and couples methane oxidation to denitrification through a newly discovered intra-aerobic pathway. In the present study, we report the first ultrastructural study of "Ca. Methylomirabilis oxyfera" using scanning electron microscopy, transmission electron microscopy, and electron tomography in combination with different sample preparation methods. We observed that "Ca. Methylomirabilis oxyfera" cells possess an atypical polygonal shape that is distinct from other bacterial shapes described so far. Also, an additional layer was observed as the outermost sheath, which might represent a (glyco)protein surface layer. Further, intracytoplasmic membranes, which are a common feature among proteobacterial methanotrophs, were never observed under the current growth conditions. Our results indicate that "Ca. Methylomirabilis oxyfera" is ultrastructurally distinct from other bacteria by its atypical cell shape and from the classical proteobacterial methanotrophs by its apparent lack of intracytoplasmic membranes. © 2012, American Society for Microbiology.

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